license: mit
language: en
FPbase: The Fluorescent Protein Database
More than 1000 experimental fluorescent proteins with structured and searchable fluorescence polarization (FP) data https://www.fpbase.org.
Quickstart Usage
installation
$ pip install fpbase
fetch database information
Run the pull_fpbase.py
$python /src/pull_fpbase.py
Output description
Check the fpbase_raw.csv
- name: protein name
- fpbase_id: ID in FPbase
- ex_max: excitation maximum
- em_max: emission maximum
- emhex: emission color
- exhex: emission color
- ext_coeff: extinction coefficient
- qy: quantum yield
- lifetime_ns: lifetime(ns)
- pdb: PDB ID:
- genbank: genbank ID
- uniprot: Uniprot ID
- aggregation: oligomeric state
- switch_type: photo-switching types
Dataset Description
(https://github.com/tlambert03/FPbase) FPbase is a free and open-source, community-editable database for fluorescent proteins (FPs) and their properties. The primary objective is to aggregate structured and searchable FP data that is of interest to the imaging community and FP developers. Each protein in the database has a dedicated page showing amino acid sequence, accession IDs (e.g. GenBank, UniProt), evolution lineages and mutations, fluorescence attributes, structural data, references that introduced or characterized the protein, and more. Excerpts from primary literature can be entered to store key information about a protein that is otherwise difficult to capture within the current database schema.